As a fuel cell system equipped with an electric storage device as an auxiliary power source of a fuel cell, there has been known one disclosed in, for example, the publication of Japanese Patent Application Laid-Open No. H09-231991. This publication discloses a fuel cell system applied to an automobile, which is a mobile body. According to the invention disclosed in the publication, when the system is started, a warm-up operation, which expedites heat generation, is performed by operating the fuel cell at low efficiency, and during the warm-up operation period, power is supplied to a motor serving as a drive device from a secondary cell, which is an electric storage device. While the secondary cell is supplying power to the motor, a warm-up state detecting means detects the warm-up state of the fuel cell during the warm-up period. If it is determined from the result of the detection that the fuel cell has been sufficiently warmed up, then the fuel cell and the motor is electrically connected so as to supply power to the motor from the fuel cell. According to the system, the fuel cell and the motor are connected after sufficient warming up is detected, thus advantageously restraining a voltage drop caused by a low temperature of the fuel cell.